3IP4

The high resolution structure of GatCAB

Summary for 3IP4

• Entry DOI: 10.2210/pdb3ip4/pdb
• Descriptor: Glutamyl-tRNA(Gln) amidotransferase subunit A, Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B, Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit C, ... (5 entities in total)
• Functional Keywords: multi protein complex, ligase, atp-binding, nucleotide-binding, protein biosynthesis
• Biological source: Staphylococcus aureus subsp. aureus; More
• Total number of polymer chains: 3
• Total formula weight: 118957.08

Authors

Nakamura, A.,Yao, M.,Tanaka, I. (deposition date: 2009-08-17, release date: 2009-11-24, Last modification date: 2023-11-01)

Primary citation

Nakamura, A.,Sheppard, K.,Yamane, J.,Yao, M.,Soll, D.,Tanaka, I.
Two distinct regions in Staphylococcus aureus GatCAB guarantee accurate tRNA recognition
Nucleic Acids Res., 38:672-682, 2010

PubMed Abstract: In many prokaryotes the biosynthesis of the amide aminoacyl-tRNAs, Gln-tRNA(Gln) and Asn-tRNA(Asn), proceeds by an indirect route in which mischarged Glu-tRNA(Gln) or Asp-tRNA(Asn) is amidated to the correct aminoacyl-tRNA catalyzed by a tRNA-dependent amidotransferase (AdT). Two types of AdTs exist: bacteria, archaea and organelles possess heterotrimeric GatCAB, while heterodimeric GatDE occurs exclusively in archaea. Bacterial GatCAB and GatDE recognize the first base pair of the acceptor stem and the D-loop of their tRNA substrates, while archaeal GatCAB recognizes the tertiary core of the tRNA, but not the first base pair. Here, we present the crystal structure of the full-length Staphylococcus aureus GatCAB. Its GatB tail domain possesses a conserved Lys rich motif that is situated close to the variable loop in a GatCAB:tRNA(Gln) docking model. This motif is also conserved in the tail domain of archaeal GatCAB, suggesting this basic region may recognize the tRNA variable loop to discriminate Asp-tRNA(Asn) from Asp-tRNA(Asp) in archaea. Furthermore, we identified a 3(10) turn in GatB that permits the bacterial GatCAB to distinguish a U1-A72 base pair from a G1-C72 pair; the absence of this element in archaeal GatCAB enables the latter enzyme to recognize aminoacyl-tRNAs with G1-C72 base pairs.

PubMed: 19906721
DOI: 10.1093/nar/gkp955

Experimental method

X-RAY DIFFRACTION (1.9 Å)